[ensembl-dev] How to get 3'UTRs of D. virilis
manakov at ebi.ac.uk
Fri Feb 17 02:35:12 GMT 2012
Thanks for directing me to metazoa.ensembl.org. Using information on
that page, I was indeed able to connect to drosophila_virilis database
and retrieve its genes.
However, there seem to be no 3'UTRs available for any of the genes in
D.viri. I don't think that FlyBase annotates transcripts beyond
exon/intron information. So what is the best way to get some kind of
3'UTRs for D.viri?
I think one way to approach this could be to use compara and 3'UTRs
of D.melanogaster (there are 3'UTRs in D.melanogaster Ensembl genes)
to get regions of homology in D.viri. Did somebody perhaps already do
Or maybe there is a different way to get D.viri 3'UTRs?
On 16 February 2012 12:19, Daniel Lawson <lawson at ebi.ac.uk> wrote:
> Dear Sergei,
> The other drosopholids are part of Ensembl Genomes and you can use the same
> scripts/mart queries to get UTRs or flanking sequences from them.
> See metazoa.ensembl.org.
> On 16 February 2012 19:53, Sergei Manakov <manakov at ebi.ac.uk> wrote:
>> I Drosophila melanogaster is in the core Ensembl, so it is
>> straightforward to get it's UTRs (both positions, sequences and gene
>> But what about other Drosophilas (I am interested in D. virilis): they
>> are not in the core Ensembl, maybe they are in compara? If so, does
>> somebody perhaps already have a script that fetches UTRs of other
>> Drosophilas? This would be very much appreciated!
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